def __init__(self, ispec, parent=None, dla_fit_file=None,
zqso=None, outfil=None, smooth=3., dw=0.1,
skip_wveval=False, norm=True):
QtGui.QMainWindow.__init__(self, parent)
"""
ispec : Spectrum1D or specfil
dla_fit_file: str, optional
Name of the LLS fit file to input
smooth : float, optional
Number of pixels to smooth on (FWHM)
dw : float, optional
Pixel width in Angstroms for the wavelength array used to
generate optical depths. Default is 0.1.
skip_wveval : bool, optional
Skip rebinning of wavelengths in the Voigt profile generation.
This can speed up the code considerably, but use it wisely.
norm : bool, optional
Whether to normalize the spectrum by dividing by the
continuum (default True).
"""
# Build a widget combining several others
self.main_widget = QtGui.QWidget()
# Status bar
self.create_status_bar()
# Initialize
if outfil is None:
self.outfil = 'DLA_fit.json'
else:
self.outfil = outfil
self.count_dla = 0
self.dla_model = None
self.smooth = None
self.base_continuum = None
self.all_forest = []
self.flag_write = False
self.dw = float(dw)
self.skip_wveval = skip_wveval
self.zqso = zqso
if skip_wveval:
warnings.warn("Skipping wavelength rebinning in Voigt.")
warnings.warn("Make sure you know what you are doing!")
# Spectrum
if isinstance(ispec, XSpectrum1D):
spec = ispec
spec_fil = spec.filename
else:
spec, spec_fil = ltgu.read_spec(ispec)
self.spec = spec
# LineList
self.llist = ltgu.set_llist('Strong')
self.llist['z'] = 0.
self.plt_wv = zip(np.array([972.5367,1025.7222,1215.6700])*u.AA,
['Lyg','Lyb','Lya'])
# z and N boxes
self.zwidget = ltgsm.EditBox(-1., 'z_DLA=', '{:0.5f}')
self.Nwidget = ltgsm.EditBox(-1., 'NHI=', '{:0.2f}')
self.bwidget = ltgsm.EditBox(-1., 'b=', '{:0.1f}')
self.Cwidget = ltgsm.EditBox('None', 'Comment=', '{:s}')
# Grab the pieces and tie together
self.abssys_widg = xspw.AbsSysWidget([],only_one=True,
no_buttons=True, linelist=self.llist[self.llist['List']])
self.spec_widg = ltgsp.ExamineSpecWidget(spec,status=self.statusBar,
llist=self.llist, key_events=False,
abs_sys=self.abssys_widg.abs_sys,
plotzero=1, norm=norm)
# Initialize continuum (and LLS if from a file)
if dla_fit_file is not None:
self.init_DLA(dla_fit_file,spec)
else:
if zqso is not None:
co, knots = laco.find_continuum(spec, redshift=self.zqso)
else:
co, knots = laco.find_continuum(spec, kind='default')
self.conti_dict = dict(co=co, knots=knots)
self.update_conti()
#self.spec_widg.continuum = self.continuum
# Full Model (LLS+continuum)
self.full_model = XSpectrum1D.from_tuple((
spec.wavelength,np.ones(len(spec.wavelength))))
if self.smooth is None:
self.smooth = smooth
# Initialize as needed
if dla_fit_file is not None:
self.update_boxes()
self.update_model()
# Outfil
wbtn = QtGui.QPushButton('Write', self)
wbtn.setAutoDefault(False)
wbtn.clicked.connect(self.write_out)
#self.out_box = QtGui.QLineEdit()
#self.out_box.setText(self.outfil)
#self.connect(self.out_box, QtCore.SIGNAL('editingFinished ()'), self.set_outfil)
# Quit
buttons = QtGui.QWidget()
wqbtn = QtGui.QPushButton('Write\n Quit', self)
wqbtn.setAutoDefault(False)
wqbtn.clicked.connect(self.write_quit)
qbtn = QtGui.QPushButton('Quit', self)
qbtn.setAutoDefault(False)
qbtn.clicked.connect(self.quit)
# Connections (buttons are above)
self.spec_widg.canvas.mpl_connect('key_press_event', self.on_key)
self.abssys_widg.abslist_widget.itemSelectionChanged.connect(
self.on_list_change)
self.connect(self.Nwidget.box,
QtCore.SIGNAL('editingFinished ()'), self.setbzN)
self.connect(self.zwidget.box,
QtCore.SIGNAL('editingFinished ()'), self.setbzN)
self.connect(self.bwidget.box,
QtCore.SIGNAL('editingFinished ()'), self.setbzN)
self.connect(self.Cwidget.box,
QtCore.SIGNAL('editingFinished ()'), self.setbzN)
# Layout
anly_widg = QtGui.QWidget()
anly_widg.setMaximumWidth(400)
anly_widg.setMinimumWidth(250)
# Write/Quit buttons
hbox1 = QtGui.QHBoxLayout()
hbox1.addWidget(wbtn)
hbox1.addWidget(wqbtn)
hbox1.addWidget(qbtn)
buttons.setLayout(hbox1)
# z,N
zNwidg = QtGui.QWidget()
hbox2 = QtGui.QHBoxLayout()
hbox2.addWidget(self.zwidget)
hbox2.addWidget(self.Nwidget)
hbox2.addWidget(self.bwidget)
zNwidg.setLayout(hbox2)
#vbox.addWidget(self.pltline_widg)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(zNwidg)
vbox.addWidget(self.Cwidget)
vbox.addWidget(self.abssys_widg)
vbox.addWidget(buttons)
anly_widg.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.spec_widg)
hbox.addWidget(anly_widg)
self.main_widget.setLayout(hbox)
# Point MainWindow
self.setCentralWidget(self.main_widget)
#self.spec_widg.setFixedWidth(900)
self.spec_widg.setMinimumWidth(900)
def __init__(self,
ispec,
parent=None,
dla_fit_file=None,
zqso=None,
outfil=None,
smooth=3.,
dw=0.1,
skip_wveval=False,
norm=True):
QtGui.QMainWindow.__init__(self, parent)
"""
ispec : Spectrum1D or specfil
dla_fit_file: str, optional
Name of the LLS fit file to input
smooth : float, optional
Number of pixels to smooth on (FWHM)
dw : float, optional
Pixel width in Angstroms for the wavelength array used to
generate optical depths. Default is 0.1.
skip_wveval : bool, optional
Skip rebinning of wavelengths in the Voigt profile generation.
This can speed up the code considerably, but use it wisely.
norm : bool, optional
Whether to normalize the spectrum by dividing by the
continuum (default True).
"""
# Build a widget combining several others
self.main_widget = QtGui.QWidget()
# Status bar
self.create_status_bar()
# Initialize
if outfil is None:
self.outfil = 'DLA_fit.json'
else:
self.outfil = outfil
self.count_dla = 0
self.dla_model = None
self.smooth = None
self.base_continuum = None
self.all_forest = []
self.flag_write = False
self.dw = float(dw)
self.skip_wveval = skip_wveval
self.zqso = zqso
if skip_wveval:
warnings.warn("Skipping wavelength rebinning in Voigt.")
warnings.warn("Make sure you know what you are doing!")
# Spectrum
if isinstance(ispec, XSpectrum1D):
spec = ispec
spec_fil = spec.filename
else:
spec, spec_fil = ltgu.read_spec(ispec)
self.spec = spec
# LineList
self.llist = ltgu.set_llist('Strong')
self.llist['z'] = 0.
self.plt_wv = zip(
np.array([972.5367, 1025.7222, 1215.6700]) * u.AA,
['Lyg', 'Lyb', 'Lya'])
# z and N boxes
self.zwidget = ltgsm.EditBox(-1., 'z_DLA=', '{:0.5f}')
self.Nwidget = ltgsm.EditBox(-1., 'NHI=', '{:0.2f}')
self.bwidget = ltgsm.EditBox(-1., 'b=', '{:0.1f}')
self.Cwidget = ltgsm.EditBox('None', 'Comment=', '{:s}')
# Grab the pieces and tie together
self.abssys_widg = xspw.AbsSysWidget(
[],
only_one=True,
no_buttons=True,
linelist=self.llist[self.llist['List']])
self.spec_widg = ltgsp.ExamineSpecWidget(
spec,
status=self.statusBar,
llist=self.llist,
key_events=False,
abs_sys=self.abssys_widg.abs_sys,
plotzero=1,
norm=norm)
# Initialize continuum (and LLS if from a file)
if dla_fit_file is not None:
self.init_DLA(dla_fit_file, spec)
else:
if zqso is not None:
co, knots = laco.find_continuum(spec, redshift=self.zqso)
else:
co, knots = laco.find_continuum(spec, kind='default')
self.conti_dict = dict(co=co, knots=knots)
self.update_conti()
#self.spec_widg.continuum = self.continuum
# Full Model (LLS+continuum)
self.full_model = XSpectrum1D.from_tuple(
(spec.wavelength, np.ones(len(spec.wavelength))))
if self.smooth is None:
self.smooth = smooth
# Initialize as needed
if dla_fit_file is not None:
self.update_boxes()
self.update_model()
# Outfil
wbtn = QtGui.QPushButton('Write', self)
wbtn.setAutoDefault(False)
wbtn.clicked.connect(self.write_out)
#self.out_box = QtGui.QLineEdit()
#self.out_box.setText(self.outfil)
#self.connect(self.out_box, QtCore.SIGNAL('editingFinished ()'), self.set_outfil)
# Quit
buttons = QtGui.QWidget()
wqbtn = QtGui.QPushButton('Write\n Quit', self)
wqbtn.setAutoDefault(False)
wqbtn.clicked.connect(self.write_quit)
qbtn = QtGui.QPushButton('Quit', self)
qbtn.setAutoDefault(False)
qbtn.clicked.connect(self.quit)
# Connections (buttons are above)
self.spec_widg.canvas.mpl_connect('key_press_event', self.on_key)
self.abssys_widg.abslist_widget.itemSelectionChanged.connect(
self.on_list_change)
self.connect(self.Nwidget.box, QtCore.SIGNAL('editingFinished ()'),
self.setbzN)
self.connect(self.zwidget.box, QtCore.SIGNAL('editingFinished ()'),
self.setbzN)
self.connect(self.bwidget.box, QtCore.SIGNAL('editingFinished ()'),
self.setbzN)
self.connect(self.Cwidget.box, QtCore.SIGNAL('editingFinished ()'),
self.setbzN)
# Layout
anly_widg = QtGui.QWidget()
anly_widg.setMaximumWidth(400)
anly_widg.setMinimumWidth(250)
# Write/Quit buttons
hbox1 = QtGui.QHBoxLayout()
hbox1.addWidget(wbtn)
hbox1.addWidget(wqbtn)
hbox1.addWidget(qbtn)
buttons.setLayout(hbox1)
# z,N
zNwidg = QtGui.QWidget()
hbox2 = QtGui.QHBoxLayout()
hbox2.addWidget(self.zwidget)
hbox2.addWidget(self.Nwidget)
hbox2.addWidget(self.bwidget)
zNwidg.setLayout(hbox2)
#vbox.addWidget(self.pltline_widg)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(zNwidg)
vbox.addWidget(self.Cwidget)
vbox.addWidget(self.abssys_widg)
vbox.addWidget(buttons)
anly_widg.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.spec_widg)
hbox.addWidget(anly_widg)
self.main_widget.setLayout(hbox)
# Point MainWindow
self.setCentralWidget(self.main_widget)
#self.spec_widg.setFixedWidth(900)
self.spec_widg.setMinimumWidth(900)
def __init__(self, ispec, parent=None, dla_fit_file=None,
zqso=None, outfil=None, smooth=None, dw=0.1, zdla=None,
NHI=None,
skip_wveval=False, norm=True, conti_file=None):
QMainWindow.__init__(self, parent)
"""
ispec : Spectrum1D or specfil
dla_fit_file: str, optional
Name of the LLS fit file to input
smooth : float, optional
Number of pixels to smooth on (FWHM). Will not smooth if 0.
dw : float, optional
Pixel width in Angstroms for the wavelength array used to
generate optical depths. Default is 0.1.
skip_wveval : bool, optional
Skip rebinning of wavelengths in the Voigt profile generation.
This can speed up the code considerably, but use it wisely.
norm : bool, optional
Whether to normalize the spectrum by dividing by the
continuum (default True).
conti_file : str, optional
ASCII file containing the continuum knots (wave, flux)
zdla : float, optional
Create a DLA at the input redshift
"""
self.help_message = """
Begin by left-clicking in the plot window!
Then any of the following keystroke commands will work:
i,o : zoom in/out x limits
I,O : zoom in/out x limits (larger re-scale)
Y : zoom out y limits
y : guess y limits
W : Show original zooom
t,b : set y top/bottom limit
l,r : set left/right x limit
a,m,d : Add/modify/delete continuum knot
A : Add a new DLA
g : Move nearest Lyman line to cursor and reset z
N/n : Increase/decrease NHI
V/v : Increase/decrease bvalue
Z/z : Increase/decrease zabs
U/u : Increase/decrease sig_NHI [Default is 0.1 dex]
D : Delete DLA
$ : Toggle displaying metal lines
6,7,8,9 : Add forest lines
? : Print these help notes
P : Save current screen in dla_plot.pdf
Q : Quit the GUI
"""
# Build a widget combining several others
self.main_widget = QWidget()
# Status bar
self.create_status_bar()
# Initialize
self.update = True
self.sig_NHI = 0.1
if outfil is None:
self.outfil = 'DLA_fit.json'
else:
self.outfil = outfil
self.count_dla = 0
self.dla_model = None
if smooth is None:
self.smooth = 3. # Pixels to smooth model by
else:
self.smooth = smooth
self.base_continuum = None
self.all_forest = []
self.flag_write = False
self.dw = float(dw)
self.skip_wveval = skip_wveval
self.zqso = zqso
if skip_wveval:
warnings.warn("Skipping wavelength rebinning in Voigt.")
warnings.warn("Make sure you know what you are doing!")
# Spectrum
if isinstance(ispec, XSpectrum1D):
spec = ispec
spec_fil = spec.filename
else:
kwargs = {}
kwargs['rsp_kwargs'] = {}
kwargs['rsp_kwargs']['masking'] = 'edges'
spec, spec_fil = ltgu.read_spec(ispec, norm=norm, **kwargs)
self.spec = spec
# LineList
self.llist = ltgu.set_llist('Strong')
self.llist['z'] = 0.
self.plt_wv = zip(np.array([972.5367,1025.7222,1215.6700])*u.AA,
['Lyg','Lyb','Lya'])
# z and N boxes
self.zwidget = ltgsm.EditBox(-1., 'z_DLA=', '{:0.5f}')
self.Nwidget = ltgsm.EditBox(-1., 'NHI=', '{:0.2f}')
self.bwidget = ltgsm.EditBox(-1., 'b=', '{:0.1f}')
self.Cwidget = ltgsm.EditBox('None', 'Comment=', '{:s}')
# Grab the pieces and tie together
self.abssys_widg = ltgsp.AbsSysWidget([],only_one=True,
no_buttons=True, linelist=self.llist[self.llist['List']])
self.spec_widg = ltgsp.ExamineSpecWidget(spec,status=self.statusBar,
llist=self.llist, key_events=False,
abs_sys=self.abssys_widg.abs_sys,
plotzero=1, norm=norm)
# Create a DLA?
if zdla is not None:
self.add_DLA(zdla, NHI=NHI, model=False)
# Initialize continuum (and DLA if from a file)
if dla_fit_file is not None:
self.init_DLA(dla_fit_file,spec)
else:
if conti_file is not None:
# Read continuum
cspec = lsi.readspec(conti_file)
if not cspec.sig_is_set:
cspec.sig = 0.1*np.median(cspec.flux)
else:
cspec = spec
if zqso is not None:
co, knots = laco.find_continuum(cspec, redshift=self.zqso)
else:
co, knots = laco.find_continuum(cspec, kind='default')
self.conti_dict = dict(co=co, knots=knots)
self.update_conti()
#self.spec_widg.continuum = self.continuum
# Full Model (LLS+continuum)
self.full_model = XSpectrum1D.from_tuple((
spec.wavelength,np.ones(len(spec.wavelength))))
# Initialize as needed
if (dla_fit_file is not None) or (zdla is not None):
self.update_boxes()
self.update_model()
# Outfil
wbtn = QPushButton(self)
wbtn.setText('Write')
wbtn.setAutoDefault(False)
wbtn.clicked.connect(self.write_out)
#self.out_box = QtGui.QLineEdit()
#self.out_box.setText(self.outfil)
#self.connect(self.out_box, QtCore.SIGNAL('editingFinished ()'), self.set_outfil)
# Quit
buttons = QWidget()
wqbtn = QPushButton(self)
wqbtn.setText('Write\n Quit')
wqbtn.setAutoDefault(False)
wqbtn.clicked.connect(self.write_quit)
qbtn = QPushButton(self)
qbtn.setText('Quit')
qbtn.setAutoDefault(False)
qbtn.clicked.connect(self.quit)
# Connections (buttons are above)
self.spec_widg.canvas.mpl_connect('key_press_event', self.on_key)
self.abssys_widg.abslist_widget.itemSelectionChanged.connect(
self.on_list_change)
self.Nwidget.box.textChanged[str].connect(self.setbzN)
self.zwidget.box.textChanged[str].connect(self.setbzN)
self.bwidget.box.textChanged[str].connect(self.setbzN)
self.Cwidget.box.textChanged[str].connect(self.setbzN)
# Layout
anly_widg = QWidget()
anly_widg.setMaximumWidth(400)
anly_widg.setMinimumWidth(250)
# Write/Quit buttons
hbox1 = QHBoxLayout()
hbox1.addWidget(wbtn)
hbox1.addWidget(wqbtn)
hbox1.addWidget(qbtn)
buttons.setLayout(hbox1)
# z,N
zNwidg = QWidget()
hbox2 = QHBoxLayout()
hbox2.addWidget(self.zwidget)
hbox2.addWidget(self.Nwidget)
hbox2.addWidget(self.bwidget)
zNwidg.setLayout(hbox2)
#vbox.addWidget(self.pltline_widg)
vbox = QVBoxLayout()
vbox.addWidget(zNwidg)
vbox.addWidget(self.Cwidget)
vbox.addWidget(self.abssys_widg)
vbox.addWidget(buttons)
anly_widg.setLayout(vbox)
hbox = QHBoxLayout()
hbox.addWidget(self.spec_widg)
hbox.addWidget(anly_widg)
self.main_widget.setLayout(hbox)
# Point MainWindow
self.setCentralWidget(self.main_widget)
#self.spec_widg.setFixedWidth(900)
self.spec_widg.setMinimumWidth(900)
# Print help message
print(self.help_message)